Re: [Ifeffit] Ifeffit Digest, Vol 73, Issue 24

Hi Damdin,

I checked my spectra and found that I forgot to do the dead time correction (measurement were in fluorescence mode). So I think the small S02 and N are due to deadtime effect.

Yes, a slightly saturated detector can cause an S02 that is a little smaller than normal.

It is possible to do it in Athena?

In general, athena doesn't have buttons or a page to do dead time corrections. This is because there isn't a single, consistent way to store the dead time information. You might want to consult with the beamline scientist for how to make these corrections. If you know what columns in your data file hold the dead time information (and what the columns are holding), it's possible to do this with Ifeffit commands (within athena, even). Cheers, --Matt Newville <newville at cars.uchicago.edu> On Mon, Mar 30, 2009 at 8:30 AM, Zuzaan, Damdinsuren wrote:

Hello everyone,

Shelly, Matt, Scott many thanks for your reply.

Damdin

-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request@millenia.cars.aps.anl.gov Sent: Saturday, March 28, 2009 6:00 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 73, Issue 24

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Today's Topics:

  1. Re: About S02 (Matt Newville)   2. Re: About S02 (Scott Calvin)

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Message: 1 Date: Fri, 27 Mar 2009 16:28:46 -0500 From: Matt Newville Subject: Re: [Ifeffit] About S02 To: XAFS Analysis using Ifeffit Message-ID:         Content-Type: text/plain; charset=ISO-8859-1

Damdin,

An XAFS book or theory that says "S02 must be between 0.8 and 1" overstates the case.

In simplest terms, S02 is a fudge factor.  There is a theoretical basis for it (passive electron overlap), but much of this can also be folded into other "loss terms" that are due to inelastic scattering events for the photo-electron.  These should be part of the EXAFS calculation from, say, Feff, but are hard to do well to high precision.  When using Feff, Ifeffit, Artemis, it does turn out that, in most cases, the calculated amplitudes tend to overestimate the experimental amplitudes, and that applying a constant S02 between 0.8 and 1.0 works reasonably well.  That is hardly a "must be" between 0.8 and 1.

In addition to the theoretical issues of Feff not-quite-correctly calculating S02, there are experimental factors that affect the XAFS amplitude: the estimate of the edge step being the most important, but also the energy resolution of the incident x-rays and sample-dependent issues such as pinholes, and for fluorescence measurements detector deadtime and self-absorption.

There is an understandable desire to turn these observation into a rule-of-thumb and then into some sort of rule that can be pointed to as if to say "this analysis is wrong" or "this analysis is correct". As is normal for such rules-of-thumb, it is sometimes broken.

Of course the main trouble with the uncertainty of which S02 to use is that for a single-shell analysis, one cannot distinguish S02 from the coordination number.  That is, the EXAFS amplitude for S02=1, N=4 is the same as for S02=0.8, N=5, and for  S02=0.67, N=6.  Distinguishing these cases is hard (don't let anyone tell you they aren't or that there is a button in Artemis that fixes this problem).   If you need to distinguish N=5 from N=6, you better be pretty confident that your data and analysis have a good value for S02.

The classic approach to this is to measure a data on a "standard" is free from amplitude-reducing artifacts and for which the coordination number is well-defined as easy to extract from the data, measure this at the same beamline conditions (energy resolution, harmonic content) as your unknown sample, and then work to be highly consistent in setting the edge step.   The S02 applied to the standard to get the correct coordination number is then applied to the unknown data to get its coordination number.     There are many ways for such an analysis to fall short of perfect, but it is generally the best we can do.

--Matt

On Fri, Mar 27, 2009 at 8:19 AM, Zuzaan, Damdinsuren wrote:

...

Hello everyone,

I am graduate student and doing EXAFS in my research.

My question is about S02. From the XAFS books or theory it says that this value must be between 0.8 to 1, but in the literature some people used different values like 0.25 or 1.4. In my case I fitted experimental RDF of my standard sample by holding the known r and n values for each path, while varying E0, S02 and sigma2. Obtained E0 and S02 values were holded for unknown sample and rest were floated freely. S02 were 0.64. So my question is that this relatively small S02 value could affect the mineralogical interpretations made in my study. Should I refit it using high value? Thanks in advance

Regards,

Damdin

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Message: 2 Date: Fri, 27 Mar 2009 19:23:29 -0400 From: Scott Calvin Subject: Re: [Ifeffit] About S02 To: XAFS Analysis using Ifeffit Message-ID: Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

Hi Damdin,

Matt and Shelly have answered this very well, but I have one more thought to add.

You have a mineralogical sample and apparently have a pretty good idea what the mineral is, since you're not varying r or n. Under those circumstances, you probably have a hypothesis as to the structure beyond the nearest-neighbor. If you include more than one path in your fit, the inability to distinguish coordination number from S02 is reduced, and more importantly for your purposes, the correlation between S02 and sigma2 is also reduced. If it stays the same when you add more paths, it can help increase your confidence that the low S02 in your fit is appropriate.

--Scott Calvin Sarah Lawrence College

On Mar 27, 2009, at 9:19 AM, Zuzaan, Damdinsuren wrote:

...

Hello everyone,

I am graduate student and doing EXAFS in my research.

My question is about S02. From the XAFS books or theory it says that this value must be between 0.8 to 1, but in the literature some people used different values like 0.25 or 1.4. In my case I fitted experimental RDF of my standard sample by holding the known r and n values for each path, while varying E0, S02 and sigma2. Obtained E0 and S02 values were holded for unknown sample and rest were floated freely. S02 were 0.64. So my question is that this relatively small S02 value could affect the mineralogical interpretations made in my study. Should I refit it using high value? Thanks in advance

Regards,

Damdin

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End of Ifeffit Digest, Vol 73, Issue 24 ***************************************

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